Methods and devices involving oil matrices

ABSTRACT

Methods for preserving viability of plant tissues such as plant embryos are provided herein. Also included are methods for storing genomic DNA and/or molecular marker assay materials in an oil bilayer as part of a high-throughput molecular characterization system. Moreover, plant embryos may be treated while in an oil matrix. The treatment may include chromosome doubling,  Agrobacterium -mediated transformation, or herbicide selection as part of an embryo rescue process.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. National application Ser.No. 14/473,183, filed Aug. 29, 2014, and of U.S. National ApplicationNo. 14/473,114, filed Aug. 29, 2014, which are incorporated by referencein their entirety.

BACKGROUND

Present conventional seed analysis methods used in genetic, biochemical,or phenotypic analysis, require at least a part of the seed to beremoved and processed. In removing some seed tissue, various objectivesmay need to be met. These may include one or more of the followingobjectives:

(a) maintain seed viability after collection of seed tissue, ifrequired,

(b) obtain at least a minimum required amount of tissue, withoutaffecting viability,

(c) obtain tissue from a specific location on the seed, often requiringthe ability to orient the seed in a specific position,

(d) maintain a particular throughput level for efficiency purposes,

(e) reduce or virtually eliminate contamination, and

(f) allow for the tracking of separate tissues and their correlation toseeds from which the tissues were obtained.

Current conventional seed testing technologies do not address theserequirements sufficiently, resulting in pressures on capital and laborresources, and thus illustrate a need in the art to provide seedanalysis methods in which the maximum number of objectives is realized.It would also be beneficial if the seed analysis methods could be usedin conjunction with other methods in the seed production process.

SUMMARY

Methods for storing, treating and selecting plant embryos are providedherein. Methods for storing genomic DNA and molecular marker assaymaterials in an oil bilayer for use in high-throughput molecularanalysis are also provided. Moreover, methods for treating plant embryoswhile in an oil matrix are provided, the treatment of which may bechromosome doubling, Agrobacterium-mediated transformation, or herbicideselection as part of an embryo rescue process.

In some embodiments, plant embryos may be stored by suspending the plantembryos or plant embryonic tissue in an aqueous solution surrounded by amatrix of one or more oils. Preferably, at least one of the one or moreoils has a density greater than that of the aqueous solution. In someaspects, antimicrobial agents and/or minimal growth media may be addedto the aqueous solution. In other aspects, the plant embryos or plantembryonic tissue may be stored in cold (preferably 4° C.) and/or darkconditions to prevent premature germination. In some embodiments, theplant embryos or plant embryonic tissue may be transferred for continuedstorage. In other embodiments, the plant embryos may be transferred togermination medium, and one or more of the plant embryos may begerminated. In still other embodiments, an aliquot of the aqueoussolution may be removed, genetic material may be obtained from cellularmaterial in the aliquot, and the genetic material may be used formolecular analysis (e.g. to genotype the stored plant embryos). Themolecular analysis may be genotyping, which may occur by way of: singlenucleotide polymorphism detection, restriction fragment lengthpolymorphism identification, random amplified polymorphic detection,amplified fragment length polymorphism detection, polymerase chainreaction, DNA sequencing, whole genome sequencing, allele specificoligonucleotide probes, or DNA hybridization to DNA microarrays orbeads. In other embodiments, one or more of the steps described abovemay be automated.

In some embodiments, methods of storing genomic DNA are provided inwhich genomic DNA, immersed in an aqueous solution, is placed betweentwo oils, one being more dense than water and the other being less densethan water. The genomic DNA in between the oil layers may be storedunder light or dark conditions. The genomic DNA in between the oillayers may be stored at a temperature between room temperature andapproximately −25 degrees Celsius, or preferably at approximately −20degrees Celsius. The methods may further comprise removing an aliquot ofsaid genomic DNA as part of an automated process to perform a molecularanalysis such as but not limited to genotyping.

In some embodiments, methods of storing molecular marker assaymaterials, immersed in an aqueous solution, are provided in whichgenomic DNA is placed between two oils, one being more dense than waterand the other being less dense than water. Molecular marker assaymaterials may comprise primers and probes. The molecular marker assaymaterials located between the oil layers may be stored under light ordark conditions. The molecular marker assay materials located betweenthe oil layers may be stored at a temperature between room temperatureand −25 degrees Celsius. The methods may further comprise removing analiquot of said molecular marker assay materials as part of an automatedprocess to perform a molecular analysis such as but not limited togenotyping.

In some embodiments, methods of treating plant embryos with a doublingagent are provided. The methods comprise placing doubling media inbetween two oils, wherein one of the oils is more dense than water andthe other is less dense than water; placing one or more plant embryos inthe doubling media for 8-48 hours under light conditions; selectingplant embryos; and transferring the selected plant embryos to media forgermination or storage. The plant embryos may be haploid. Moreover, analiquot of the media may be removed, genetic material may be obtainedfrom cellular material in the aliquot, and the genetic material may beused for molecular analysis (e.g. to genotype the treated plantembryos). The molecular analysis may be genotyping,

In some embodiments, methods of selecting plant embryos during doubledhaploid production are provided. In the methods, (a) doubling media isplaced between two oils, in which one of the oils is more dense thanwater and the other is less dense than water; (b) the plant embryos areplaced in the doubling media for 8-48 hours under light conditions, and(c) plant embryos are selected for germination or storage. Between steps(b) and (c), cellular material may be collected from the one or moreplant embryos; DNA may be obtained from the cellular material; andgenotypic information may be obtained, allowing selection of one or moreembryos based on genotypic information. The methods may further comprisetransferring the selected plant embryos to media for germination orstorage. The doubling media may comprise an anti-microtubule agent. Thedoubling media may comprise colchicine, pronamide, dithipyr,amiprophosmethyl or trifluralin. The plant embryos placed in thedoubling media may be haploid.

In some embodiments, the plant embryos are maize haploid embryosproduced by a cross between a male inducer line and a female line ofinterest, in which the male inducer line contains a marker gene that isexpressed in embryo tissue. The marker gene may express anthocyaninpigments, which are only expressed in the diploid embryos. Thus, whiteembryos that do not express anthocyanin may further be selected fortransfer to media for germination or storage. The selection may beperformed using a camera or other imaging device. The methods mayfurther comprise germinating or storing the selected embryos.

To facilitate selection of the white embryos, the expression ofanthocyanin may be enhanced by aeration of the doubling media or byplacing the plant embryos in a hypotonic doubling media comprisingperfluorodecalin (PFC).

In some embodiments, methods of transforming plant tissue are providedin which a suspension comprising Agrobacterium tumefaciens, whichcomprises within its genome a recombinant DNA construct comprising oneor more genes of interest and a selectable marker gene, between twooils, in which one oil is more dense than water and the other is lessdense than water; placing the plant tissue in the suspension; removingthe plant tissue from said suspension and cultivating the plant tissuein media; resting the plant tissue in media; and placing the planttissue in contact with media comprising a selection agent correspondingto the selectable marker gene. The method may further compriseregenerating a plant from said plant tissue, wherein said plant tissueis a plant embryo or plant callus. The plant tissue may be stored insaid suspension for up to one hour. Step (d) may comprise resting theplant tissue in media in the dark at a temperature of about 28 degreesCelsius for a period of up to 14 days. The media comprising theselection agent corresponding to the selectable marker gene may belocated between two oils, wherein one of the oils is more dense thanwater and the other is less dense than water.

In some embodiments, methods of incubating plant tissue in a solutioncomprising a selection agent are provided in which the plant tissue insaid solution is located between two oils, wherein one of the oils ismore dense than water and the other is less dense than water. Theselection agent may be glyphosate, glufosinate, bialaphos, hygromycin B,kanamycin, paromomycin, mannose, phosphinothricin, butafenacil, orR-haloxyfop. The method may further include selecting plant tissue thatremains viable following incubation. The plant tissue may be a plantembryo or plant callus.

DETAILED DESCRIPTION

Plant breeding programs can benefit from preservation of viable plantsources, which may include keeping the viable plant sources in a mannerthat preserves an ability to be grown into a plant as well as keepingthe viable plant sources in a manner that prevents germination. Onebenefit can be seen in that genetic material can be obtained formolecular characterization, allowing selections to be made prior togrowing the plant. Additional benefits may include treating haploidplant embryos with chromosome doubling agents while being preserved ortransforming viable plant sources while being preserved.

Viable plant sources may be seeds, plant embryos, plant tissue, or wholeplants. Most typically, viable plant sources are capable of being growninto plants, although not necessarily. Preservation of seeds typicallyrequires no particular care. When the viable plant sources are embryos,however, special care should be taken to preserve viability.

In one preferred method, plant embryos are suspended in an aqueoussolution surrounded by a matrix of one or more oils. Oil having adensity less than water will cover the plant embryo(s) in the aqueoussolution, while oil having a density greater than water will support theplant embryo(s) in the aqueous solution. In some embodiments, the one ormore plant embryos is suspended in an aqueous solution surrounded by amatrix of two or more oils, wherein at least one of the two or more oilsis more dense than the aqueous solution and at least one of the two ormore oils is less dense than the aqueous solution, further wherein theaqueous solution is surrounded by the oil that is more dense than theaqueous solution and the oil that is less dense than the aqueoussolution. In some embodiments, antimicrobial agents and/or minimalgrowth media may be added to the aqueous solution. In some embodiments,the plant embryos may be stored in cold and/or dark conditions toprevent premature germination. In a preferred embodiment, the plantembryos are stored at a temperature of approximately 4° C. In someembodiments, the plant embryos may be transferred for continued storage.In other embodiments, the plant embryos may be transferred togermination medium, and the plant embryos may be germinated. In apreferred embodiment, an aliquot of the aqueous solution may be removed;genetic material may be obtained from cellular material in the aliquot;and the genetic material may be used for molecular analysis (e.g. togenotype the stored plant embryos).

High density oil that may be used in this method includes but is notlimited to perfluoro compounds having 12 compounds (e.g., DuPont's lowerviscosity KRYTOX® oils). Low density oil that may be used in this methodincludes but is not limited to phenylmethylpolysiloxane. Other non-toxicoils known to those of ordinary skill in the art may be used instead ofor in combination with these compounds.

Obtaining Genetic Material for Molecular Characterization

In order for genetic material to be analyzed, it must be freed from thecell such that it is accessible for molecular analysis. This may involvephysical treatments such as exposure to cold-heat or just heat,incubation with enzymes, or even DNA extraction techniques (although itis important to note that extraction is not a necessary step inobtaining DNA for molecular analysis). Essentially any process thatdisrupts the tissue and breaks open cells, thereby releasing DNA thatcan be used for molecular characterization, may be used in the methodsprovided herein.

In some embodiments, DNA may be obtained from the cellular material byexposing the cellular material to cold-heat or heat, agitating themixture, and optionally repeating. In other embodiments, DNA may beobtained by incubating cellular material with an enzyme; the enzyme maybe VISCOZYME® L, a multi-enzyme complex containing a wide range ofcarbohydrases, including arabanase, cellulase, β-glucanase,hemicellulase, and xylanase. (See the Sigma Aldrich product catalog). Instill other embodiments, obtaining DNA may comprise extraction of theDNA, such as through the use of magnetic particles that bind geneticmaterial or any method known to one of ordinary skill in the art.However, extraction is not necessary for obtaining DNA.

Molecularly Characterizing the Genetic Material from the Multiple ViablePlant Sources

In cases where the yield of DNA obtained from embryo tissue is notsufficient for some molecular analysis (e.g. high density genotyping),whole genome amplification techniques may be used. The Qiagen REPLI-gkit, the Sigma-Aldrich SeqPlex kit, or any other technique known to oneof ordinary skill in the art may be used to amplify DNA from plantembryonic tissue.

Other useful molecular characterizations may involve sequencing all orpart of the genome of the tissue extracted from the seed, or usingmolecular markers and fluorescent probes to genotype. Molecularcharacterization need not focus on the genotype of the extracted tissue,but instead may measure other properties such as oil content, oilcomposition, protein content, or the presence or absence of particularmolecules in the tissue.

In a preferred embodiment, genetic material is placed in a well of amultiple well plate containing a bilayer of oil, one layer having adensity greater than water and one layer having a density less thanwater. Multiple wells contain multiple different genetic materials.Fluorescently labeled probes are added to the genetic materials, andthermocycling to cause amplification and hybridization of the probes isperformed in the multiple well plate. The wells are irradiated andfluorescence is detected from the labels to generate genotypic data.Alternatively, the genetic material may be sequenced, in whole or inpart, in the multiple well plate.

Genomic DNA and/or molecular marker assay materials (such as but notlimited to primers and probes) may also be stored in a bilayer of oil tofacilitate automation and high-throughput molecular characterization. Inboth instances, the materials are immersed in an aqueous solution, whichis placed between two oils, one being more dense than water and theother being less dense than water. Storage of genomic DNA and/ormolecular marker assay materials may be in light or dark conditions andmay occur at approximately 4 degrees Celsius or at room temperature.Storage in this manner allows a mechanical device to obtain aliquotsfrom stored genomic DNA and from stored molecular marker assay materialsand combine them in a reaction mixture in order to performhigh-throughput molecular characterization.

Selecting One or More Viable Plant Sources

In a molecular breeding program, plants or potential plants are selectedto participate in subsequent generations based on their genotype.Typically this involves determining whether the plant has inherited oneor more desirable traits indicated by genetic markers whose presence orabsence can be determined based on the genotyping. Plant breeders selectthose plants that have the desired traits to participate in furtherbreeding, to inbreed, or as part of a process to create inbreds throughhaploid doubling techniques. Those plants that are selected based on thepresence of desirable traits as determined by their genotype may begrown into mature plants, to obtain haploid material to create a doublehaploid inbred, to breed with itself to create an inbred, or to breedwith other plants to improve and diversify germ plasm.

The plant embryo storage methods described above allow genotypicinformation to be obtained for plant embryos that are being stored,allowing embryos to be selected based on genotypic information.

The plant embryo storage methods may also be used to treat plant embryoswhile the plant embryos are stored (short-term or long-term) in an oilmatrix.

One treatment may be the doubling of plant embryos with a doublingagent. In the methods, doubling media is placed between two oils,wherein one of the oils is more dense than water and the other is lessdense then water; the plant embryos are placed in doubling media for8-48 hours under light conditions; plant embryos are selected; and theselected plant embryos are transferred to media for germination orstorage. The plant embryos may further be germinated or stored. Theplant embryos may be haploid. Genetic material may be obtained from theplant embryos and the plant embryos may be molecularly characterized(e.g. genotyping). Selections of the plant embryos may be based ongenotypic information.

Methods of chromosome doubling in maize are disclosed inAntoine-Michard, S. et al., Plant cell, tissue organ cult., Cordrecht,the Netherlands, Kluwer Academic Publishers, 1997, 48(3):203-207; Kato,A., Maize Genetics Cooperation Newsletter 1997, 36-37; Wan, Y. et al.,TAG, 1989, 77: 889-892. Wan, Y. et al., TAG, 1991, 81: 205-211; U.S.Pat. No. 8,865,971; and U.S. Pat. No. 8,404,930; the disclosures ofwhich are incorporated herein by reference. Typical methods involvecontacting the cells with colchicine, anti-microtubule agents oranti-microtubule herbicides, pronamide, nitrous oxide, or any mitoticinhibitor to create homozygous doubled haploid cells. The amount ofcolchicine used in medium is generally 0.01%-0.2% or approximately 0.05%or APM (5-225 μM). The amount of colchicine can range from approximately100-600 mg/L, and preferably may be approximately 500 mg/L. The amountof pronamide in medium is approximately 0.5-20 μM. Other agents may beused with the mitotic inhibitors to improve doubling efficiency. Suchagents may be dimethyl sulfoxide (DMSO), adjuvants, surfactants, and thelike.

In some embodiments, methods of selecting plant embryos during doubledhaploid production are provided. In the methods, (a) doubling media isplaced between two oils, in which one of the oils is more dense thanwater and the other is less dense than water; (b) the plant embryos areplaced in the doubling media for 8-48 hours under light conditions, and(c) plant embryos are selected. Between steps (b) and (c), cellularmaterial may be collected from the one or more plant embryos; DNA may beobtained from the cellular material; and genotypic information may beobtained, allowing selection of one or more embryos based on genotypicinformation. The methods may further comprise transferring the selectedplant embryos to media for germination or storage and/or germinating theplant embryos. The doubling media may comprise an anti-microtubuleagent. The doubling media may comprise colchicine, pronamide, dithipyr,amiprophosmethyl or trifluralin. The plant embryos placed in thedoubling media may be haploid.

Maize haploid embryos may be produced by a cross between a male inducerline and a female line of interest, in which the male inducer linecontains a marker gene that is expressed in embryo tissue. The markergene may express anthocyanin pigments, which are only expressed in thediploid embryos. Thus, white embryos that do not express anthocyanin mayfurther be selected for transfer to media for germination or storage.The selection may be performed using a camera or other imaging device.

In the above, expression of anthocyanin (or the observation thereof) maybe enhanced by aeration of the doubling media. This may occur by shakingthe liquid media prior to contact with the plant embryos or by bubblingfiltered air through the three layers (first oil layer, liquid medium,second oil layer) since the phase separation would occur once the airsupply is shut down. Another method involves placing the plant embryosin a hypotonic doubling media comprising perfluorodecalin (PFC). Thehypotonic doubling media may also comprise bleach to reduce bacterialgrowth.

The female line of interest may or may not be an inbred and may have adesirable genetic makeup. The female line of interest may also comprisewithin its genome one or more transgenes of interest.

The haploid inducer lines described herein have incorporated anthocyanincolor markers incorporated into their genomes; the markers are expressedboth within the kernel pericarp and in the scutellum. The color markersare used to screen the embryos. Haploid embryos lack the paternal genewith the color marker and therefore appear white or colorless.

One of the limitations of using liquid media is that the color markerfails to be expressed when the embryos are submerged in the medium andtherefore it is difficult to separate diploids from haploids embryosafter doubling. To overcome this limitation, methods to increasedissolved oxygen content within the media may be used to enhance thelevel of anthocyanin expression or the observation thereof. In methodsdescribed herein, anthocyanin expression in liquid media may be enhancedby incubating the embryos in hypotonic liquid media consisting ofperfluorodecalin (PFC), a liquid saturated in oxygen, and 0.1%commercial bleach (5% NaOCl v/v), by shaking, and/or by bubbling themedium with filtered air (aeration). Enhancement of anthocyaninexpression in liquid media may be performed while the liquid media islocated between oils in an oil matrix; however, it is not necessary forthe liquid media to be between oils. Selection is facilitated whether ornot the liquid media is located between oils in an oil matrix. Moreover,the use of the hypotonic doubling media comprising perfluorodecalin(PFC) to enhance anthocyanin expression is not exclusive to liquid mediaand may be used to eliminate diploid embryos regardless of how the plantembryos are being stored.

Another treatment may be the transformation of plant tissue withAgrobacterium tumefaciens, which has within its genome a recombinant DNAconstruct that comprises one or more genes of interest and a selectablemarker gene. The methods include placing a suspension containing theAgrobacterium between two oils, in which one oil is more dense thanwater and the other is less dense than water; placing the plant tissuein the suspension; removing the plant tissue from the suspension andcultivating the plant tissue in media; resting the plant tissue in themedia; and placing the plant tissue in contact with media comprising aselection agent corresponding to the selectable marker gene. The methodmay further comprise regenerating a plant from said plant tissue, whichmay be a plant embryo or plant callus. The plant tissue may be stored inthe suspension for up to one hour. “Resting” may comprise placing theplant tissue in media in the dark at a temperature of about 28 degreesCelsius for a period of up to 14 days. The media comprising theselection agent may also be located between two oils, wherein one of theoils is more dense than water and the other is less dense than water.However, the step of selecting the embryos can also be performed inmedia that is not located within an oil matrix.

The benefits to performing Agrobacterium-mediated transformation ofembryos in an oil matrix are simplification of the downstream multipleculturing process, amenability for automation, a reduction in costspertaining to consumables, and a reduction in consumable waste.

Another treatment may be the incubation of plant tissue in a solutioncontaining a selection agent. This also may be done while the planttissue is located between two oils, wherein one of the oils is moredense than water and the other is less dense than water. The selectionagent may be glyphosate, glufosinate, bialaphos, hygromycin B,kanamycin, paromomycin, mannose, phosphinothricin, butafenacil, orR-haloxyfop. The method may further include selecting plant tissue thatremains viable following incubation. The plant tissue may be a plantembryo or plant callus. This method may be used to determine whetherplant tissue includes a native trait that confers the ability towithstand the selection agent.

While the examples provided herein relate to a monocot, specificallymaize, those of ordinary skill in the art would understand how to applythe same or similar methods to other monocots and dicots; the methodsmay be adapted to any plant. For instance, the plant may include but isnot limited to maize, soybean, sunflower, sorghum, canola, wheat,alfalfa, cotton, rice, barley, millet, sugar cane, or switchgrass.

EXAMPLE 1 Embryo Genotyping in Maize

A. Collection of Maize Embryo Material:

Maize embryos were washed 3 times using 2 mL of sterile water. Maizeembryos were incubated in a tube containing either 10 μL, 20 μL, 50 μL,75 μL, or 150 μL of sterile water for either 10 minutes, 20 minutes, orovernight. It was found that adequate genotyping data can be obtainedwith any of the dilution volumes, and that 10 minutes was a sufficientincubation time. All protocols for washing and incubating the maizeembryos were used with all three tissue collection methods describedbelow.

Method 1: The tubes containing the maize embryos were agitated viatapping 10 times and were then spun down in a tabletop centrifuge for 5seconds. The water was then removed from each tube for analysis. It wasfound that this method achieved the best results for genotyping.

Method 2: Maize embryos were washed 3 times using 2 mL of sterile water.The maize embryos were incubated in a tube containing 50 μL of sterilewater for 10 minutes. The water was then removed from the tube foranalysis.

Method 3: Maize embryos were washed 3 times using 2 mL of sterile water.The maize embryos were incubated in a tube containing 50 μL of sterilewater for 10 minutes. Tubes containing the maize embryos were agitatedvia tapping 10 times. The water was then removed from each tube foranalysis.

B. Methods to obtain DNA:

Cold-Heat Shock:

Maize embryonic material obtained using all three methods describedabove was placed in a −80° C. freezer for 20 min; then placed on athermocycler at 100° C. for 10 min and pipetted up and down to mix. Theprocess was repeated for a total of two rounds. The resulting mixtureswere stored at −20° C. It was found that the best results for genotypingwere achieved from DNA obtained using this method.

Heat Shock Only:

Maize embryonic tissues were placed on a thermocycler at 100° C. for 10min and pipetted up and down to mix. The process was repeated for atotal of two rounds. The mixtures were stored at −20° C.

Enzymatic Method:

The mixtures from the preceding step were incubated in a 95° C. oven toevaporate off the remaining water. 18.0 μL of PBS solution and 2.0 μL ofdiluted VISCOZYME® L (commercially available from Sigma-Aldrich; diluted1:200 in PBS Solution pH 7.4; total vol. 20 μL) were added and themixtures were incubate at 37° C. for 2 hours. A quantity of 2.0 μL ofdiluted proteinase K (commercially available from Sigma-Aldrich; diluted1:20 in PBS Solution pH 7.4) was added and the mixtures were incubatedat 55° C. for 50 minutes then heated to 95° C. for 10 min. The mixtureswere stored at −20° C.

DNA Extraction:

The mixtures from the methods of Example 1B were incubated in a 95° C.oven to evaporate off the remaining water. 45 μL Lysis buffer PN (LGCGenomics) was added to each mixture, each of which was centrifugedbriefly and incubated at 65° C. for 1 hour. To new tubes were added 60μL Binding buffer PN, 5 μL Sbeadex particles (magnetic particles thatbind genetic material, which are commercially available from LGCGenomics) followed by the lysate mixtures, which were then incubated atroom temperature for 4 minutes to allow binding of DNA to the particles,vortexed briefly and placed in a magnetic rack to concentrate beads. Thelysis buffer was removed and 100 μL wash buffer PN1 (LGC Genomics) wasadded to resuspend the beads. Washing was repeated using 100 μL washbuffer PN2 (LGC Genomics) followed by a 100 μL pure water wash. 10 μLelution buffer PN was added and the mixtures were incubated at 55° C.for 10 minutes with vortexing every 3 minutes. The magnetic rack wasused to concentrate beads and the eluate was transferred to new tubesand stored at −20° C.

C. Whole Genome Amplification

When whole genome amplification was required the following protocol wasfollowed using the REPLI-g® Single Cell Kit (commercially available fromQiagen). Whole genome amplification was done to achieve higher DNA yieldand to facilitate the detection of high density marker sets.

2.5 μL template DNA was combined with 2.5 μL Buffer D1 (commerciallyavailable from Qiagen; total volume 5.0 μL) and incubated at roomtemperature for 3 minutes. 5.0 μL Buffer N1 (commercially available fromQiagen; total volume 10.0 μL) was added and the mixtures were vortexedand centrifuged briefly. A Master Mix containing 9.0 μL nuclease-freewater, 29.0 μL REPLI-g® Reaction Buffer (commercially available fromQiagen) and 2.0 μL REPLI-g® DNA Polymerase (commercially available fromQiagen) was used per reaction to give 50.0 μL total volume. The mixtureswere run on a thermocycler using a 30° C. for 8 hours and 4° C.thereafter. DNA quantitation was performed using a Qubit assay(commercially available from Life Technologies). The DNA product wasused directly in the genotyping step.

D. Molecular Analysis

TAQMAN® Marker Analysis

Marker analysis was carried out using TAQMAN® assays (commerciallyavailable from Life Technologies). DNA was diluted to a targetconcentration of 20 ng/μL. A 384 plate containing the DNA was loadedinto LC480 real-time PCR thermocycler and run using the followingprogram: pre-incubation: 1 cycle (95° C. for 5 minutes); amplification:45 cycles, (−95° C. for 30 seconds, −60° C. for 45 seconds (singleacquisition), −72° C. for 1 minute (single acquisition); cooling: 1cycle, (−72° C. for 10 minutes, −40° C. for 30 seconds). Calls were readusing Roche LC480 LightCycler® Software (commercially available fromRoche Diagnostics).

Results

The foregoing methods all gave acceptable genotyping results.

EXAMPLE 2 MaizeE Embryo StorageE

Two lines of maize germplasm were selected for testing the impacts ofextended embryo storage in an oil matrix on germination rates. Embryosfrom each line were isolated by hand before being placed into theirrespective storage condition. All embryos were plated on germinationmedia to evaluate germination rates in a controlled growth chamber. Sixembryos of each line were immediately plated on germination mediawithout any storage exposure to act as a control for germination in acontrolled growth chamber. Seventy two (72) embryos of each line wereisolated and evenly divided across three storage conditions, with adedicated storage tube for each embryo:

Storage condition 1: 24 embryos were placed in 50 μuL aqueous solutionsurrounded by two layers of oil with significantly different densities,one with a density significantly greater than water and one with adensity significantly less than water.

Storage condition 2: 24 embryos were placed in a 50 uL droplet ofaqueous solution with an added antimicrobial agent, surrounded by thetwo oils of condition 1.

Storage condition 3: 24 embryos were placed in a 50 uL droplet ofminimal growth media with an added antimicrobial agent, surrounded bythe two oils of condition 1.

All tubes were placed in a dark refrigerator at 4 degrees centigrade forthe duration of the experiment. At four (4) time points, 6 embryos ofeach line were removed from their storage condition and plated ongermination media in a controlled growth chamber to evaluate germinationrates. The time points were as follows:

Time point 1: 15 minutes after placement into storage.

Time point 2: 1 day after placement into storage.

Time point 3: 5 days after placement into storage.

Time point 4: 10 days after placement into storage.

Embryo germination rates were then monitored to determine optimalstorage conditions. It was found that germination rates were excellentfor embryos stored in each of the three storage methods.

EXAMPLE 3 GenotypingG Reagent Storage Study Methods and Materials

Two components of an endpoint SNP genotyping reaction, genomic DNA and amolecular marker assay (primers and probe), were selected to test theimpacts on reagent viability after extended storage in an oil bilayer,at various conditions.

Genomic DNA was isolated from maize leaf tissue and from maize seedtissue via known extraction protocols to evaluate the impact of extendedstorage, compared to a baseline. A volumetric subset from each tissuetype extraction was left at stock extraction concentration and theremaining volume was diluted to a factor well suited for a SNPgenotyping reaction. The DNA concentration volumes were further dividedto provide dedicated volumes for evaluating storage impacts in Light vs.Dark conditions and Room Temperature vs. 4° Celsius conditions, as wellas a combination of each.

Four molecular marker assays used for endpoint SNP genotyping of maizewere selected to evaluate impact of extended storage, compared to abaseline. A volumetric subset of each molecular marker assay was left ata stock concentration and the remaining volume of each molecular markerassay was diluted to a factor well suited for a SNP genotyping reaction.The molecular marker assay volumes were further divided to providededicated volumes for evaluating storage impacts in Light vs. Darkconditions and Room Temperature vs. 4° C. conditions, as well as acombination of each.

Prior to the volume separation steps, a baseline sample was taken fromeach reagent to generate a baseline data set for comparison at eachstorage time point. The extracted test DNA reagent was screened againsta control molecular marker assay (not the test molecular marker assay)and the test molecular marker assays were screened against control DNAsamples (not the test DNA samples). Each reagent volume was placed intoan oil bilayer prior to being stored in their respective storagecondition (Light/Dark, Room Temp/4° Celsius). At pre-defined timepoints, aliquots of reagents from each test storage condition, for eachreaction component, were taken and screened against control reagentcompliments within an endpoint SNP genotyping reaction. Genotypic datafrom all time points was compared to the baseline for reactioncompletion efficiency and overall data quality. Data quality from thestored molecular marker assay reagents was comparable to that of thebaseline.

EXAMPLE 4 Haploid Embryo Doubling and Selection in Oil Matrix

Experiments were performed to determine if doubling treatments can beapplied to embryos stored in the oil bilayer.

2×colchicine selection media consisting of: 2×DCS Media (Doubling,Colchicine, Sucrose), 2×DCS Media components (per Liter), 300.00 gSucrose Grade II, 8.67 g of MS Basal Salt Mixture, 0.80 g L-AsparagineMonohydrate, 10.00 mL 36J Vitamin Solution, 2.50 mL of ThiamineSolution, 0.20 mL of BAP Solution, 1.00 g Colchicine, 41.66 mL of DMSO(20%), and RO water to 1.00 L, was prepared. 2×colchicine selectionmedia was placed in screw-top microcentrifuge tubes and diluted with anequal amount of sterile water to 1×concentration. 50 μL of 1×liquidcolchicine selection media was added to each tube, which contained ahigh-density oil and a low-density encapsulating oil. The colchicinemedia settles between the oil layers.

Twenty embryos were rescued from an ear produced by a cross between amale inducer line, which comprises in its genome a marker gene thatexpresses anthocyanin pigments in embryo tissue, and a female line ofinterest. Embryos were transferred into the colchicine media using asterilized spatula, and tubes were placed in a lighted growth chamberroom for 8-48 hours. Embryos were selected based on the color image froma camera. Purple or diploid embryos were discarded, while the whiteembryos were transferred to growth media plates. The plates were thenplaced back in the culture chamber for germination. The germination ratefor both haploid and diploid embryos is comparable to the standardprotocol without using oil encapsulation.

EXAMPLE 5 Enhancement of Anthocyanin Expression for Improved Selection

In the methods described in Example 5, the level of anthocyaninexpression can be enhanced, resulting in improved selection. Either ofthe methods described below, as well as other methods known to one ofordinary skill in the art, may be used to increase dissolved oxygencontent within the media, thereby enhancing the level of anthocyaninexpression or the observation thereof.

In one experiment, the culture media was aerated prior to introducingthe embryo into the oil matrix environment. Four mL of culture media ina 50 mL Falcon tube was prepared and placed in a rocker table at maximumspeed for several hours. The media was immediately transferred into oilmatrix tubes after aeration. The results indicate that the oxygen levelin the medium facilitates the detection of anthocyanin coloration forthe diploid embryos. Alternatively, liquid medium could also be aeratedby bubbling filtered air through the three layers (first oil layer,liquid medium, second oil layer) since the phase separation would occuronce the air supply is shut down.

In another experiment, embryos were incubated in a hypotonic liquidmedium consisting of PFC (perfluorodecalin; undiluted and in whatevervolume needed to cover the embryo) and 0.1% commercial bleach (5% NaOClv/v). The addition of bleach was sufficient to inhibit bacterial growthwithout affecting germination when compared to the control. Anthocyanincolor appeared at the border of the scutellum within 12 hours of thecolchicine treatment and then continued centripetally until the wholeembryo became purple-red (if diploid). Germination in liquid medium isstatistically similar to the control using solid medium.

EXAMPLE 6 Agrobacterium-Mediated Transformation of Maize Embryos in anOilMatrix

An Agrobacterium suspension may be prepared (such as shown in U.S. Pat.No. 5,981,840) and then placed between two oils, one of which is moredense than water and the other of which is less dense than water. TheAgrobacterium-containing suspension would settle between the oil layers.

Embryos are isolated and then placed in the Agrobacterium-containingsuspension, which is located between the oil layers, for 5 minutes. Theembryos are then removed from the Agrobacterium-containing suspensionand then cultivated for 2-4 days. For the resting step, embryos aretransferred to a new plate and incubated in the dark at approximately28° C. for up to 14 days, in order to eliminate any remainingAgrobacterium. For selection, embryos are then placed in contact withmedia containing a selection agent that corresponds to the selectablemarker gene inserted into the vector in the Agrobacterium, in order tokill any non-transformation events. The selection step can also takeplace in media located between two oils in an oil matrix. Thetransformed cells are then regenerated to form whole plants using tissueculture methods.

The benefit of allowing transformation of the embryo to occur while inmedia surrounded by the oil bilayer is to simplify the downstreammultiple culturing process. The system is more automatable than theconventional methods transferring cultivates using agar based medium andwould reduce the cost of consumables as well as the associated waste.

EXAMPLE 7 Trait Selection of Maize Embryos in Oil Matrix

Effective selection is one of the most critical steps in selectingplants and plant tissues that contain a transgene or native trait ofinterest. The presence of a selecting agent allows for the proliferationof transgenic tissues and at the same time suppresses or killsuntransformed tissue. Similarly, a selecting agent may be used todetermine whether a plant tissue includes a native trait that confersthe ability to withstand the selection agent. The ideal selection agentshould not have a negative impact on subsequent regeneration, rootingand plant growth. Both antibiotics and herbicides can be used asselection agents. Commonly used agents include glyphosate, glufosinate,bialaphos, hygromycin B, kanamycin, paromomycin, mannose,phosphinothricin, butafenacil and R-haloxyfop.

Transformed plant tissue or plant tissue having a resistance trait, suchas a plant embryo, can be placed in media comprised of MS salts 4.3 g/l;myo-inositol 0.1 g/l; Thiamine.HCL 0.1 mg/l, Pyridoxine.HCl 0.5 mg/l,Glycine 2.0 mg/l, nicotinic acid 0.5 mg/l and sucrose 40.0 g/l at a pHof 5.6. The selection agent can be added directly to such media and thenthe media containing the agent, along with the plant tissue, can belocated between two oils, wherein one of the oils is more dense thanwater and the other is less dense than water.

Plant Embryos may be transferred into the selection-containing mediausing a sterilized spatula, and the embryos in the selection-containingmedia located between the two oils are placed at 8 degrees C. to 26degrees C. for up to 7 days for selection. Only embryos that have withintheir genomes genes that confer tolerance to the selection agent willsurvive. Image selection based on morphological differences, for exampleby machine vision and computer processing, may be used to differentiatethe viable embryos from the dead embryos.

We claim:
 1. A method of storing genomic DNA, said method comprisingplacing the genomic DNA, immersed in an aqueous solution, between twooils, wherein one of the oils is more dense than water and the other isless dense than water.
 2. The method of claim 1, wherein said genomicDNA is stored under light or dark conditions.
 3. The method of claim 1,wherein said genomic DNA is stored at a temperature between roomtemperature and −25 degrees Celsius.
 4. The method of claim 1, furthercomprising removing an aliquot of said genomic as part of an automatedprocess to perform a molecular analysis.
 5. A method of storingmolecular marker assay materials, said method comprising placing themolecular marker assay materials, immersed in an aqueous solution,between two oils, wherein one of the oils is more dense than water andthe other is less dense than water.
 6. The method of claim 5, whereinsaid molecular marker assay materials comprise primers and probes. 7.The method of claim 5, wherein said molecular marker assay materials arestored under light or dark conditions.
 8. The method of claim 5, whereinsaid molecular marker assay materials are stored at a temperaturebetween room temperature and −25 degrees Celsius.
 9. The method of claim5, further comprising removing an aliquot of said molecular marker assaymaterials as part of an automated process to perform a molecularanalysis.
 10. A method of treating one or more plant embryos with adoubling agent, said method comprising: a. placing doubling mediabetween two oils, wherein one of the oils is more dense than water andthe other is less dense than water; b. placing one or more plant embryosin the doubling media ; c. selecting one or more plant embryos; and d.transferring the selected plant embryos to media for germination orstorage.
 11. The method of claim 10, wherein said one or more plantembryos are haploid embryos.
 12. The method of claim 10, wherein betweensteps (c) and (d) cellular material is collected from the one or moreplant embryos; DNA is obtained from the cellular material; and genotypicinformation is obtained from the one or more plant embryos.
 13. Themethod of claim 12, wherein said plant embryos are selected based ongenotypic information.
 14. A method of selecting one or more plantembryos during doubled haploid production, said method comprising: a.placing doubling media between two oils, wherein one of the oils is moredense than water and the other is less dense than water; b. placing oneor more plant embryos in the doubling media and c. selecting one or moreplant embryos for germination or storage.
 15. The method of claim 14,wherein between steps (b) and (c) cellular material is collected fromthe one or more plant embryos; DNA is obtained from the cellularmaterial; and genotypic information is obtained from the one or moreplant embryos.
 16. The method of claim 15, wherein said one or moreplant embryos are selected based on genotypic information.
 17. Themethod of claim 16, further comprising transferring the selected plantembryos to media for germination or storage.
 18. The method of claim 14,wherein said doubling media comprises an anti- microtubule agent. 19.The method of claim 14, wherein said doubling media comprisescolchicine, pronamide, dithipyr, am iprophosmethyl or trifluralin. 20.The method of claim 14, wherein said one or more plant embryos arehaploid.
 21. The method of claim 14, wherein said one or more plantembryos in step (c) are haploid maize embryos produced by a crossbetween a male inducer line and a female line of interest.
 22. Themethod of claim 21, wherein said male inducer line contains a markergene that is expressed in embryo tissue.
 23. The method of claim 22,wherein said marker gene expresses anthocyanin pigments.
 24. The methodof claim 23, wherein plant embryos that are white are selected to betransferred to media for germination or storage.
 25. The method of claim24, wherein selection of the white plant embryos is performed using acamera or other imaging device.
 26. The method of claim 24, whereinexpression of anthocyanin is enhanced by aeration of the doubling media.27. The method of claim 24, wherein expression of anthocyanin isenhanced by placing the plant embryos in a hypotonic doubling mediacomprising perfluorodecalin.
 28. The method of claim 24, furthercomprising germinating or storing the selected plant embryos.
 29. Amethod of transforming plant tissue, said method comprising: a. forminga suspension comprising Agrobacterium tumefaciens, wherein saidAgrobacterium tumefaciens comprises within its genome a recombinant DNAconstruct comprising one or more genes of interest and a selectablemarker gene, between two oils, wherein one of the oils is more densethan water and the other is less dense than water; b. placing the planttissue in said suspension; c. removing the plant tissue from saidsuspension and cultivating the plant tissue in media; d. resting theplant tissue in media; and e. placing the plant tissue in contact withmedia comprising a selection agent corresponding to the selectablemarker gene.
 30. The method of claim 29, further comprising regeneratinga plant from said plant tissue.
 31. The method of claim 29, wherein theplant tissue is a plant embryo or plant callus.
 32. The method of claim29, wherein the plant tissue is stored in said suspension for up to onehour.
 33. The method of claim 29, wherein step (d) comprises resting theplant tissue in media in the dark at a temperature of about 28 degreesCelsius for a period of up to 14 days.
 34. The method of claim 29,wherein said media comprising a selection agent corresponding to theselectable marker gene is located between two oils, wherein one of theoils is more dense than water and the other is less dense than water.35. A method comprising incubating plant tissue in a solution betweentwo oils, wherein one of the oils is more dense than water and the otheris less dense than water, the solution comprising a selection agent. 36.The method of claim 35, wherein the selection agent is glyphosate,glufosinate, bialaphos, hygromycin B, kanamycin, paromomycin, mannose,phosphinothricin, butafenacil, or R-haloxyfop.
 37. The method of claim35, further comprising the step of selecting plant tissue that remainsviable after said incubating step.
 38. The method of claim 35 whereinthe plant tissue is a plant embryo or plant callus.